Biology subjects

Comte, S.

Publications and source records attributed to Comte, S..

6 recordsLinked to original sources

bioRxiv2026

Wildlife disease surveillance under uncertainty: an adaptive search-theoretic framework for early detection of transboundary animal diseases

Rapid detection is critical for successful management of transboundary animal disease incursions in wild host populations. However, decisions about how best to allocate wildlife disease surveillance effort must be made under high uncertainty. Risk-based surveillance can improve efficiency but approaches that focus surveillance too narrowly on expected high risk areas could have low power to detect unexpected events. We developed and field-tested an adaptive, search-theoretic surveillance framework for detecting transboundary animal disease incursions in wild ungulates in New South Wales, Australia. Key principles that guided the frameworks development included accommodating uncertainty, regularly updating search priorities based on expected risk and spatial coverage, and a flexible structure that allows the system to respond to changing information or conditions over time. We created a coarse state-wide risk map that served as a weakly informative prior describing expected variability in disease incursion risk, loosely focused on foot and mouth disease virus (FMDv). Risk and search values were updated every three months based on realised surveillance effort and estimated detection probabilities over the preceding 12 months, meaning that areas of persistently high risk could nonetheless have low search value if they had recently been intensively searched. Surveillance activities collected blood and swab samples from 1,964 wild pigs (Sus scrofa) during 110 sampling occasions over a two-year evaluation and refinement period. Activities sought to simulate FMDv surveillance operations, but FMDv serological tests were not available at the time. Effort was consistently concentrated in areas of high search value, with at least 74% of sampled cells in the highest risk class. Estimated surveillance system sensitivity ranged from 0.86 to 0.93 over five successive updating cycles and increased as operational procedures were refined. Although the surveillance program was based on FMDv incursion risk, it also fulfilled its secondary objective of detecting unexpected events, including detecting Japanese encephalitis virus in wild pigs before detections in humans and domestic animals. By combining risk-based surveillance with adaptive updating of search priorities in a modular structure, the framework provided a flexible and generalisable approach for early detection of transboundary and emerging animal disease incursions in wildlife populations under high uncertainty.

zoology↗

bioRxiv2025

Response to "No evidence that transmissible cancer has shifted from emergence to endemism in Tasmanian devils"

Herein, we rebut the critique of Patton et al. (2020), entitled, "No evidence that a transmissible cancer has shifted from emergence to endemism", by Stammnitz et al. (2024). First and foremost, the authors do not conduct any phylogenetic or epidemiological analyses to rebut the inferences from the main results of the Patton et al. (2020) article, rendering the title of their rebuttal without evidence or merit. Additionally, Stammnitz et al. (2024) present a phylogenetic tree based on only 32 copy number variants (not typically used in phylogenetic analyses and evolve in a completely different way than DNA sequences) to "rebut" our tree that was inferred from 436.1 kb of sequence data and nearly two orders of magnitude more parsimony-informative sites (2520 SNPs). As such it is not surprising that their phylogeny did not have a similar branching pattern to ours, given that support for each branch of their tree was weak and the essentially formed a polytomy. That is, one could rotate their resulting tree in any direction and by nature, it would not match ours. While the authors are correct that we used suboptimal filtering of our raw whole genome sequencing data, re-analyses of the data with 30X coverage, as suggested, resulted in a mutation rate similar to that reported in Stammnitz et al. (2024). Most importantly, when we re-analyzed our data, as well as Stammnitz et al.s own data, the results of the Patton et al. (2020) article are supported with both datasets. That is, the effective transmission rate of DFTD has transitioned over time to approach one, suggesting endemism; and, the spread of DFTD is rapid and omnidirectional despite the observed east-to-west wave of spread. Overall, Stammnitz et al. (2024) not only fail to provide evidence to contradict the findings of Patton et al. (2020), but rather help support the results with their own data.

evolutionary biology↗

bioRxiv2024

Effects of a transmissible cancer on life-history traits in Tasmanian devils

Shifts in life history traits, such as timing of reproduction, can help mediate population declines following perturbations, and early reproduction should be favoured when adult survival is impacted more than juvenile survival. In Tasmanian devils, following the emergence of a fatal transmissible cancer, females started to breed precocially (i.e., at age one instead of typically age two) and the same time as populations started to decline following disease emergence. Here, we focus on a diseased site (Freycinet Peninsula, Tasmania, Australia) with 18 years of continuous mark-recapture data to test: (1) whether rates of precocial breeding in females continued to increase after the initial rise after the emergence of the disease, (2) whether there was a relationship between body size and breeding success for either one-year-olds or adult females (i.e., at least two-years-old), and (3) whether there was inbreeding depression in breeding success for either age category. We show that rates of precocial breeding did not continue to rise, and that the proportion of precocially breeding females has plateaued at around 50%. We also show that there was no effect of body size on the probability of breeding for either one-year-old or for adult females. Finally, we show that there was no evidence for inbreeding depression in breeding success for either age class. We discuss possible constraints that may have inhibited further rise in rates of precocial breeding in the context of limitations to growth in the offspring of precocially breeding (and therefore smaller) females.

evolutionary biology↗

bioRxiv2023

Spatial niche separation of an invasive and a native mesopredator

Re-introduced native animals face major challenges to re-establish themselves in their previous range of distribution when invasive alien predators are present. We study the interactions between a native and an invasive mesopredator across an ecological gradient in the Ikara-Flinders Ranges National Park in South Australia. We placed VHF/ GPS-collars on feral cats (Felis catus) and re-introduced western quolls (Dasyurus geoffroyi) and analysed their movement patterns, both utilisation distributions and behavioural states, and habitat selection. Despite being able to move anywhere in this open landscape, there is a clear interspecific difference between the two species in their use and preference for landscape elements. Cats prefer grassland and occupy flat areas where rabbit densities are high. Quolls prefer forests and avoid areas of high rabbit and therefore areas of high cat density. The almost complete spatial separation of cats and quolls may reflect different habitat requirements, but the historically broad distribution of quolls suggests that cats may limit quolls continuously to a restricted niche in the Flinders Ranges. This raises the possibility of management interventions that could support a further expansion of quoll occupancy.

ecology↗

bioRxiv2023

The effects of alternative rabbit control methods on feral cat activity in an open, semi-arid landscape

The availability of invasive prey often plays an important role in regulating cointroduced invasive predator populations. As predators have been shown to respond rapidly to declines in prey populations, our objective was to experimentally test how local population reduction of an invasive prey species, the European rabbit (Oryctolagus cuniculus), affects the activity of an introduced predator, the feral cat (Felis catus). To test the effectiveness of three different rabbit control methods, activity levels of cats were surveyed with remote infrared wildlife cameras in three treatment and four control sites. The rabbit control treatments were implemented in extensive open landscapes in the semi-arid zone of South Australia, and consisted of shooting of rabbits, destruction of rabbit warrens, and the targeted delivery of baits treated with RHDV. The results indicate that only the destruction of rabbit warrens has observable effects on the number of cat detections on cameras. Cat detections decreased in the areas where rabbit warrens were destroyed and increased in adjacent areas where rabbits were still abundant. This suggests that cats vacated the treated area and moved into surrounding areas of abundant introduced prey.

ecology↗

bioRxiv2022

The evolution of two transmissible cancers in Tasmanian devils

Tasmanian devils have spawned two transmissible cancer lineages, named devil facial tumour 1 (DFT1) and devil facial tumour 2 (DFT2). We investigated the genetic diversity and evolution of these clones by analysing 78 DFT1 and 41 DFT2 genomes relative to a newly assembled chromosome-level reference. Time-resolved phylogenetic trees reveal that DFT1 first emerged in 1986 (1982-1989), and DFT2 in 2011 (2009-2012). Subclone analysis documents transmission of heterogeneous cell populations. DFT2 has faster mutation rates than DFT1 across all variant classes, including substitutions, indels, rearrangements, transposable element insertions and copy number alterations, and we identify a hypermutated DFT1 lineage with defective DNA mismatch repair. Several loci show plausible evidence of positive selection in DFT1 or DFT2, including loss of chromosome Y and inactivation of MGA, but none are common to both cancers. This study illuminates the parallel long-term evolution of two transmissible cancers inhabiting a common niche in Tasmanian devils.

cancer biology↗